The abbreviated version of what I read is that the main differences are in the mane and the base, as detailed here:
L. E. Smith horses are easily identified by a knotted mane and a much thicker base than the other two. Also, the neck is thinner and not as arched. The glass quality is somewhat inferior to that of Fostoria or New Martinsville, and they are slightly less valuable.
Fostoria horses have a cropped mane which appears very slightly beaded, a Roman nose and a 1/2" wide ledge around the base. Also, the right ear is smaller than the left ear.
New Martinsville horses have a cropped mane which appears straight/squared off, a Roman nose and a 1" wide ledge around the base.
L. E. Smith
etsy.com
Fostoria
Forum - ebay.com
New Martinsville
Forum - ebay.com
I also sent an email to the curator of the Heisy Glass Museum to find out if that company produced similar rearing horse bookends, but I have not received a response yet. If I find out that they did, I will update again.
Thanks to reader Mitzy for her comment, which resulted in my finding out more than I ever thought possible about these bookends that my parents received as a gift when they were a young married couple (including the fact that they are less valuable than the others, which is too bad for me). I hope what I gleaned from my research provides some helpful information to you vintage glass shoppers/sellers.
Update 8/2/2011: I just received another email from L. E. Smith employee Patti Bryner with more information about the bookends. She said:
You are correct about the base. I don't know if Heisy made them or not. They were produced [by L. E. Smith] from May of 1945 until the early part of 2000. This book end has been attributed to the American Glass Company in the past; however, the drawing in Plate 841 [of LE Smith: The First One Hundred Years] is from an application submitted by LE Smith for wage arbitration by the National Association of Manufacturers of Pressed and Blown Glassware...Hope this helps you out. If you can, buy the book LE Smith: The First One Hundred Years. It has a lot of information about our products.